O94953 (KDM4B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Lysine-specific demethylase 4B
EC=1.14.11.-

Alternative name(s):
JmjC domain-containing histone demethylation protein 3B
Jumonji domain-containing protein 2B

Gene names

Name:	KDM4B
Synonyms:	JHDM3B, JMJD2B, KIAA0876

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	1096 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate. Ref.9
Cofactor	Binds 1 Fe2+ ion per subunit By similarity.
Subcellular location	Nucleus Ref.8.
Domain	The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails By similarity.
Sequence similarities	Belongs to the JHDM3 histone demethylase family. Contains 1 JmjC domain. Contains 1 JmjN domain. Contains 2 PHD-type zinc fingers. Contains 2 Tudor domains.
Sequence caution	The sequence AAC33799.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence BAA74899.2 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Repeat Zinc-finger
Ligand	Iron Metal-binding Zinc
Molecular function	Chromatin regulator Dioxygenase Oxidoreductase
PTM	Acetylation Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O94953-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: O94953-2)

The sequence of this isoform differs from the canonical sequence as follows:
     373-448: SHRKRSQPKK...EDGRGKLRPT → TPPCVSPHRP...LRMATQDPCR
     449-1096: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1096	1096	Lysine-specific demethylase 4B		PRO_0000183175
Regions
	Domain	15 – 57	43	JmjN
	Domain	146 – 309	164	JmjC
	Domain	917 – 974	58	Tudor 1
	Domain	975 – 1031	57	Tudor 2
	Zinc finger	731 – 789	59	PHD-type 1
	Zinc finger	851 – 907	57	PHD-type 2
	Compositional bias	463 – 535	73	Pro-rich
Sites
	Metal binding	189	1	Iron; catalytic By similarity
	Metal binding	191	1	Iron; catalytic By similarity
	Metal binding	235	1	Zinc By similarity
	Metal binding	241	1	Zinc By similarity
	Metal binding	277	1	Iron; catalytic By similarity
	Metal binding	307	1	Zinc By similarity
	Metal binding	309	1	Zinc By similarity
	Binding site	133	1	Alpha-ketoglutarate By similarity
	Binding site	199	1	Alpha-ketoglutarate By similarity
	Binding site	207	1	Alpha-ketoglutarate By similarity
Amino acid modifications
	Modified residue	305	1	Phosphothreonine By similarity
	Modified residue	566	1	Phosphoserine Ref.7 Ref.10
	Modified residue	602	1	N6-acetyllysine Ref.11
	Modified residue	622	1	Phosphoserine Ref.7
	Modified residue	1065	1	Phosphothreonine Ref.10
Natural variations
	Alternative sequence	373 – 448	76	SHRKR…KLRPT → TPPCVSPHRPSQPGIWCPPG GEAKASAASWLLTTRGHGDT EAGPGLGGDPLHAQSEGQAS CVSTSRLRMATQDPCR in isoform 2.		VSP_018307
	Alternative sequence	449 – 1096	648	Missing in isoform 2.		VSP_018308
	Natural variant	29	1	N → T. Corresponds to variant rs11667206 [ dbSNP | Ensembl ].		VAR_026223
	Natural variant	710	1	K → E. Ref.1 Ref.4 Ref.5 Ref.6 Corresponds to variant rs2620836 [ dbSNP | Ensembl ].		VAR_026224

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified March 20, 2007. Version 4. Checksum: 300D5CD6F2DD4330	FASTA	1,096	121,897
	10 20 30 40 50 60 MGSEDHGAQN PSCKIMTFRP TMEEFKDFNK YVAYIESQGA HRAGLAKIIP PKEWKPRQTY 70 80 90 100 110 120 DDIDDVVIPA PIQQVVTGQS GLFTQYNIQK KAMTVGEYRR LANSEKYCTP RHQDFDDLER 130 140 150 160 170 180 KYWKNLTFVS PIYGADISGS LYDDDVAQWN IGSLRTILDM VERECGTIIE GVNTPYLYFG 190 200 210 220 230 240 MWKTTFAWHT EDMDLYSINY LHFGEPKSWY AIPPEHGKRL ERLAIGFFPG SSQGCDAFLR 250 260 270 280 290 300 HKMTLISPII LKKYGIPFSR ITQEAGEFMI TFPYGYHAGF NHGFNCAEST NFATLRWIDY 310 320 330 340 350 360 GKVATQCTCR KDMVKISMDV FVRILQPERY ELWKQGKDLT VLDHTRPTAL TSPELSSWSA 370 380 390 400 410 420 SRASLKAKLL RRSHRKRSQP KKPKPEDPKF PGEGTAGAAL LEEAGGSVKE EAGPEVDPEE 430 440 450 460 470 480 EEEEPQPLPH GREAEGAEED GRGKLRPTKA KSERKKKSFG LLPPQLPPPP AHFPSEEALW 490 500 510 520 530 540 LPSPLEPPVL GPGPAAMEES PLPAPLNVVP PEVPSEELEA KPRPIIPMLY VVPRPGKAAF 550 560 570 580 590 600 NQEHVSCQQA FEHFAQKGPT WKEPVSPMEL TGPEDGAASS GAGRMETKAR AGEGQAPSTF 610 620 630 640 650 660 SKLKMEIKKS RRHPLGRPPT RSPLSVVKQE ASSDEEASPF SGEEDVSDPD ALRPLLSLQW 670 680 690 700 710 720 KNRAASFQAE RKFNAAAART EPYCAICTLF YPYCQALQTE KEAPIASLGK GCPATLPSKS 730 740 750 760 770 780 RQKTRPLIPE MCFTSGGENT EPLPANSYIG DDGTSPLIAC GKCCLQVHAS CYGIRPELVN 790 800 810 820 830 840 EGWTCSRCAA HAWTAECCLC NLRGGALQMT TDRRWIHVIC AIAVPEARFL NVIERHPVDI 850 860 870 880 890 900 SAIPEQRWKL KCVYCRKRMK KVSGACIQCS YEHCSTSFHV TCAHAAGVLM EPDDWPYVVS 910 920 930 940 950 960 ITCLKHKSGG HAVQLLRAVS LGQVVITKNR NGLYYRCRVI GAASQTCYEV NFDDGSYSDN 970 980 990 1000 1010 1020 LYPESITSRD CVQLGPPSEG ELVELRWTDG NLYKAKFISS VTSHIYQVEF EDGSQLTVKR 1030 1040 1050 1060 1070 1080 GDIFTLEEEL PKRVRSRLSL STGAPQEPAF SGEEAKAAKR PRVGTPLATE DSGRSQDYVA 1090 FVESLLQVQG RPGAPF
	Isoform 2 [UniParc]. Checksum: 84E9B0DEEF9C84F9	FASTA	448	50,582
	10 20 30 40 50 60 MGSEDHGAQN PSCKIMTFRP TMEEFKDFNK YVAYIESQGA HRAGLAKIIP PKEWKPRQTY 70 80 90 100 110 120 DDIDDVVIPA PIQQVVTGQS GLFTQYNIQK KAMTVGEYRR LANSEKYCTP RHQDFDDLER 130 140 150 160 170 180 KYWKNLTFVS PIYGADISGS LYDDDVAQWN IGSLRTILDM VERECGTIIE GVNTPYLYFG 190 200 210 220 230 240 MWKTTFAWHT EDMDLYSINY LHFGEPKSWY AIPPEHGKRL ERLAIGFFPG SSQGCDAFLR 250 260 270 280 290 300 HKMTLISPII LKKYGIPFSR ITQEAGEFMI TFPYGYHAGF NHGFNCAEST NFATLRWIDY 310 320 330 340 350 360 GKVATQCTCR KDMVKISMDV FVRILQPERY ELWKQGKDLT VLDHTRPTAL TSPELSSWSA 370 380 390 400 410 420 SRASLKAKLL RRTPPCVSPH RPSQPGIWCP PGGEAKASAA SWLLTTRGHG DTEAGPGLGG 430 440 DPLHAQSEGQ ASCVSTSRLR MATQDPCR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro." Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O. DNA Res. 5:355-364(1998) [PubMed: 10048485] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT GLU-710. Tissue: Brain.
[2]	"Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones." Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T. DNA Res. 9:99-106(2002) [PubMed: 12168954] [Abstract] Cited for: SEQUENCE REVISION.
[3]	"The DNA sequence and biology of human chromosome 19." Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M. Nature 428:529-535(2004) [PubMed: 15057824] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT GLU-710.
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANT GLU-710. Tissue: Testis.
[6]	"The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed: 17974005] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 487-1096, VARIANT GLU-710. Tissue: Testis.
[7]	"Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-566 AND SER-622, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[8]	"Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein." Gray S.G., Iglesias A.H., Lizcano F., Villanueva R., Camelo S., Jingu H., Teh B.T., Koibuchi N., Chin W.W., Kokkotou E., Dangond F. J. Biol. Chem. 280:28507-28518(2005) [PubMed: 15927959] [Abstract] Cited for: SUBCELLULAR LOCATION.
[9]	"Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases." Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y. Cell 125:467-481(2006) [PubMed: 16603238] [Abstract] Cited for: FUNCTION, ENZYME ACTIVITY.
[10]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-566 AND THR-1065, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[11]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-602, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB020683 mRNA. Translation: BAA74899.2. Different initiation. AC005595 Genomic DNA. Translation: AAC33799.1. Sequence problems. AC022517 Genomic DNA. Translation: AAF31271.1. CH471139 Genomic DNA. Translation: EAW69181.1. CH471139 Genomic DNA. Translation: EAW69183.1. BC063889 mRNA. Translation: AAH63889.1. BC136611 mRNA. Translation: AAI36612.1. AL133622 mRNA. Translation: CAB63748.2.
IPI	IPI00013205. IPI00440491.
PIR	T43460.
RefSeq	NP_055830.1. NM_015015.2.
UniGene	Hs.654816.
3D structure databases
ProteinModelPortal	O94953.
SMR	O94953. Positions 10-346, 755-790, 917-1034.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-47283N.
IntAct	O94953. 1 interaction.
MINT	MINT-1427202.
STRING	O94953.
PTM databases
PhosphoSite	O94953.
Proteomic databases
PRIDE	O94953.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000159111; ENSP00000159111; ENSG00000127663.
GeneID	23030.
KEGG	hsa:23030.
NMPDR	fig|9606.3.peg.15454.
UCSC	uc002mbq.2. human.
Organism-specific databases
CTD	23030.
GeneCards	GC19P004921.
HGNC	HGNC:29136. KDM4B.
MIM	609765. gene.
neXtProt	NX_O94953.
PharmGKB	PA164721452.
HUGE	Search...
GenAtlas	Search...
Phylogenomic databases
eggNOG	prNOG06475.
GeneTree	ENSGT00530000063342.
InParanoid	O94953.
OMA	MLYVVPR.
OrthoDB	EOG4N5VW5.
PhylomeDB	O94953.
Gene expression databases
ArrayExpress	O94953.
Bgee	O94953.
CleanEx	HS_JMJD2B.
Genevestigator	O94953.
Family and domain databases
InterPro	IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR003349. TF_JmjN. IPR002999. Tudor. IPR011011. Znf_FYVE_PHD. IPR001965. Znf_PHD. IPR013083. Znf_RING/FYVE/PHD. [Graphical view]
Gene3D	G3DSA:3.30.40.10. Znf_RING/FYVE/PHD. 1 hit.
KO	K06709.
Pfam	PF02373. JmjC. 1 hit. PF02375. JmjN. 1 hit. [Graphical view]
SMART	SM00558. JmjC. 1 hit. SM00545. JmjN. 1 hit. SM00249. PHD. 2 hits. SM00333. TUDOR. 2 hits. [Graphical view]
SUPFAM	SSF57903. FYVE_PHD_ZnF. 1 hit.
PROSITE	PS51184. JMJC. 1 hit. PS51183. JMJN. 1 hit. PS50304. TUDOR. False negative. PS01359. ZF_PHD_1. False negative. PS50016. ZF_PHD_2. False negative. [Graphical view]
ProtoNet	Search...
Other
SOURCE	Search...

Entry information

Entry name

KDM4B_HUMAN

Accession

Primary (citable) accession number: O94953
Secondary accession number(s): B9EGN8 , D6W631, O75274, Q6P3R5, Q9P1V1, Q9UF40

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 16, 2004
Last sequence update:	March 20, 2007
Last modified:	January 25, 2012
This is version 99 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.